Someone's not telling the truth was the only thing Metra leaders and their ex-CEO Alex Clifford agreed upon in contradictory testimony about conflicts of interest and political gravy trains during an RTA hearing Wednesday.

The Regional Transportation Authority is auditing a separation agreement criticized by some as "hush money" that could give up to $718,000 to Clifford, who made $252,000 annually.

As a sign scrutiny is increasing, Thomas Homer, the General Assembly's legislative inspector general, said Wednesday he was investigating allegations made by Clifford that he was ousted for refusing to go along with political pressure by Speaker Michael Madigan and other lawmakers over jobs and contracts at the agency in 2012.

"I have nothing to hide," said a defiant Clifford who sat just a few feet from Metra administrators. "I refused to accede to the requests of some very powerful politicians in Illinois."

"I categorically deny everything (Clifford) said," O'Halloran testified. "It's just incredible to me to be listening to this. What we heard today was a whole lot of hooey. I was the one who blew the whistle."

The commuter rail agency has been in flux since March, when a dispute over renewing Clifford's contract erupted.

Among Wednesday's surprises was Clifford's disclosure he was treated for thyroid cancer, leading Metra board member Larry Huggins to use his absence to alter a contract for the Englewood Flyover, a railway bridge on Chicago's South Side.

A lack of black contractors on the project enraged congressmen and community members who accused Metra of excluding African-Americans. Huggins intervened in the contract, which Clifford said went against federal funding guidelines.

"He's twisting things," Huggins said. "Do I apologize for trying to stand up for the African-American community and try to make sure there was inclusion? No, I do not," Huggins said. "In my opinion, it was the right thing to do."

Clifford also alleged a Metra subcontractor, the Target Group, did not perform the community outreach the company was paid $200,000 to accomplish. He noted that Huggins was a business associate of the company's owner.

Huggins said he was a business partner with the Target Group's Joseph Williams but added, "Have I committed a crime because I know Joseph? No."

Clifford also alleged that attempts were made to include a financial institution with ties to Old Plank Trail Bank in Mokena in a larger banking contract with Metra. O'Halloran is on the board of the bank.

O'Halloran said Clifford was distorting his attempts to broaden the number of banks that work for Metra. "He's taking something innocent and turning it into something untoward," he said.

Clifford said the fear of losing funding support from Madigan caused Huggins to exert "enormous pressure" to give a Madigan donor and former Metra employee, Patrick Ward, a raise and to promote another employee for a union job. Madigan has denied any wrongdoing. Clifford also said the speaker pushed for another employee to be promoted to conductor.

Meanwhile, Metra officials described an agency in turmoil with Clifford's authority restricted after they became convinced he was going to sue them, and with the former CEO spending time reviewing thousands of emails.

One of Clifford's hires, Executive Director for Administration Alex Wiggins, said his former sponsor "became obsessed with doing whatever he could to renew his contract."

Wiggins added Clifford adopted a "confrontational approach" and tried to manipulate who the next Metra chairman would be. "He forgot he was staff and thought the board worked for him."

Adding to the political allegations, Clifford described interference by state Rep. Elizabeth "Lisa" Hernandez, a Cicero Democrat, who told him during a meeting that her husband, who was a Metra employee, was being mistreated.

Hernandez could not be reached for comment.

Clifford has accused the Latino caucus, including state Rep. Luis Arroyo, a Chicago Democrat, of pressuring him to hire a Hispanic deputy executive director. He noted Wednesday that Arroyo's daughter works at Metra.

Arroyo and others have said they asked Clifford to increase Latino representation on Metra, not to hire a specific person.

When he asked about his contract renewal early in 2013, Clifford said O'Halloran responded, "I need to have a meeting with Mr. Madigan to see what damage you caused to our funding (prospects)."

But O'Halloran countered: "I never made that statement. I have no relationship with Speaker Madigan."

Clifford said it became "clear" to him that O'Halloran was "going to work very hard not to give me a new contract."

Clifford also testified O'Halloran had been making inquiries about him with former colleagues in California, where he worked as a transit executive previously.

"At this point I was steamed," he testified. It appeared "there were dirty deeds behind the scenes."

"This has been a long and difficult process," Clifford said. "It was my goal to stay with Metra and work there. It was my goal to stay until the end of my contract."

RTA directors had little comment after the marathon session, but their questions showed a variety of perspectives.

RTA Chairman John S. Gates interrogated Clifford about the glacial pace of the agency's transition to a joint fare system with Pace and the CTA, and about tardy audits.

"This the second year in a row Metra's been late with audits," he said.

Clifford told Gates' his criticisms were "unfair," adding, "Do not take this simplistic approach."

RTA Director Dwight Magalis told Clifford, "You're very straight to the point and say what you think. ... I've gained a lot of respect for your knowledge."

Director J.D. Ross was frustrated with Metra: "I don't see anything that justifies what you paid (in the settlement)," he said.

Ironically, the RTA has been swept up in Metra's scandal as its Chief of Staff Jordan Matyas is Madigan's son-in-law. Officials said he had recused himself from the agency's audit of the separation agreement.

The state's executive inspector general, Ricardo Meza, also is investigating, and Halloran asked again and again why Clifford hadn't brought his concerns to Meza.

"Why not take it to the (inspector general)?" O'Halloran asked. "He claims he was the whistle-blower. I was the first person with the whistle."

"I reported these facts to board members shortly after they occurred in 2012 and asked for guidance," Clifford said.

Metra attorneys, however, said they had reviewed executive session tapes and found no record of Clifford's discussing his concerns.

Metra Director Paul Darley is credited with bringing Clifford's allegations to O'Halloran this spring, which then resulted in their being turned over to the inspector general.

The Elmhurst businessman said he "had no idea" how political the agency could get. "The settlement was a business decision. I and other board members had come on board with the directive it should be run like a business."

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